Skin Microbiome Medicine for Dermatology - Dermatology Advisor
Breakthroughs in Skin Microbiome Medicine May Transform Dermatology
Human skin harbors complex microbial communities of bacteria, viruses, and fungi. A growing body of research shows that shifts in the species composition, diversity, and metabolic products of the skin ecosystem can open the door to invasion by harmful microbes, inflammatory responses, skin barrier dysfunction, and dermatologic disease.
"We have a complex relationship with our skin microbes, which are integral to immune homeostasis and repair, as well as mediators of local and systemic inflammation," explained Nathan Archer, PhD, assistant professor of dermatology at Johns Hopkins University School of Medicine.
The clinical implications of utilizing the skin microbiome in the treatment of dermatologic diseases could be profound.
Shifts in microbial community structure — especially reduced overall species diversity and the resulting predominance of pathogenic and pro-inflammatory species — precede the onset or worsening of symptoms in atopic dermatitis, eczema, acne, and psoriasis.1-5 Large-scale genomic sequencing has identified previously unsuspected bacterial communities and microbial signatures that can help distinguish lesional skin from healthy skin, pointing toward new diagnostic and therapeutic targets.1,5-7
Instead of viewing microbes solely as pathogens, we're beginning to harness them as therapeutic partners, designing interventions that restore microbial balance, modulate immunity, and promote repair.
Recent research has also demonstrated that disruptions of skin ecology, called dysbiosis, are more consistently associated with acne and other inflammatory dermatoses than the overgrowth of Cutibacterium acnes or Staphylococcus aureus. Dysbiosis contributes directly to disease flares, challenging longstanding assumptions about the etiology of dermatologic diseases.4,8,9 Indeed, dysbiosis appears to be a hallmark mechanism in inflammatory dermatoses like eczema, rosacea, and psoriasis, driven by altered microbiome-immune system interactions.8
Scientists are exploring how ecological engineering of the skin microbiome might offer alternatives to current therapies like antibiotics, which eradicate both pathogens and beneficial microbes and may worsen dysbiosis and induce treatment resistance.10,11
"Understanding their roles opens the door to entirely new therapeutic paradigms: instead of only suppressing inflammation, we can begin to restore balance between our skin and the microbial community," Dr Archer said.
For example, preclinical research suggests that applying commensal bacteria can improve the integrity of the skin barrier and reduce S aureus overgrowth in atopic dermatitis.10,12 Researchers are also investigating prebiotics, strain-specific probiotics, live bacteriotherapies, genetically engineered bacteriophages, and targeted phage cocktails for selectively culling pathogens from skin ecosystems.7,10,11,13
The field of microbiome dermatology is young and not without significant challenges, including the need for better standardization of research methodologies and further expansion of research ventures.4,5 Yet experts maintain optimism about knowledge gained thus far and that these challenges will be overcome. They anticipate a clinical paradigm shift toward precision microbiome medicine in the years ahead.
The Skin Microbiome Beyond the Skin
The skin's microbial ecosystem includes a dermal microbiome beneath the skin's surface and a distinct epidermal microbiome interfacing the external environment, shaped by infants' early encounters with microbes, explained Richard Gallo, MD, PhD, professor and chair of the department of dermatology at the University of California San Diego School of Medicine. Intriguingly, Dr Gallo and his colleagues found that these microbial communities communicate with the microbiomes of other organ systems, like the gut.14,15
Skin wounds affect intestinal bacteria, for example.16 "Our work discovered that injury or inflammation of the skin causes release of 'danger signals' that are detected by cells in the intestine," Dr Gallo said. "These cells then respond by producing antimicrobials that inappropriately kill some of the bacteria in the gut that help maintain gut health. This is important as it provides an explanation for the frequent co-occurrence of diseases of the skin and gut, and emphasizes the need to treat the whole patient, not just a single organ."
This skin-to-gut axis is not the only connection between skin and other microbiomes, Dr Gallo was quick to point out. "Important communication occurs between skin and lung, skin and brain, and skin and the cardiovascular system," he explained. "With continued work, we see important general medical breakthroughs coming from understanding these communication networks."
Indeed, a recent study showed that S aureus skin exposure can exacerbate lung inflammation, helping to explain the atopic march from atopic dermatitis to respiratory disease.17
"Clinically, this highlights the importance of early intervention in atopic dermatitis — addressing microbial dysbiosis and interleukin (IL)-36-driven inflammation before diseases of the atopic march develop, such as asthma," said Dr Archer.
For patients with overlapping atopic dermatitis and neutrophilic asthma, that finding bolsters the case for a more integrated clinical approach to achieve better outcomes, Dr Archer added. "Rather than treating skin and airway disease in isolation, clinicians might consider shared immunological pathways as therapeutic targets or agents that modulate or restore healthy microbial balance that could, in principle, benefit both skin and lung inflammation," he said.
Biomarkers like IL-36 and neutrophil signatures might be helpful for risk assessment and early therapeutic escalation in patients with atopic dermatitis, to prevent neutrophilic asthma progression, Dr Archer added.
"Elevated systemic IL-36 and neutrophil signatures could identify patients whose atopic dermatitis may be leading towards neutrophilic asthma or T2-low asthma, which is more treatment-resistant than T2-high asthma," he explained. "In fact, circulating IL-36 has already been associated with severe asthma in patients."
With his coauthors, Dr Archer also reported that bacteria like S aureus can promote skin regeneration through IL-1β-dependent signaling pathways, with important implications for wound care.18
"This suggests that indiscriminate topical antibiotic use may disrupt beneficial microbe-host interactions that aid healing," Dr Archer explained. "Microbiome-aware wound care that balances pathogen control with preservation of beneficial microbes may improve regenerative outcomes."
Atopic dermatitis and asthma are heterogeneous conditions with immunological subtypes, Dr Archer pointed out, and better understanding of their mechanistic underpinnings will enable the development of more personalized treatment approaches.
"Understanding which cytokine and microbial pathways drive an individual's disease — whether it be IL-36–neutrophil, Th2, or S aureus — may enable personalized therapy selection and better prediction of comorbidities like asthma or food allergy," Dr Archer said. "We are moving away from a one-size-fits-all mentality and entering an era of precision dermatology. Instead of viewing microbes solely as pathogens, we're beginning to harness them as therapeutic partners, designing interventions that restore microbial balance, modulate immunity, and promote repair."
Are Skin Diseases Industrial Comorbidities?
In addition to genomics and molecular mechanism studies, insights into healthy skin microbiomes are being gleaned from cross-cultural research.
"Over the last few decades we've seen a steady rise in chronic inflammatory skin conditions, especially in Western countries and in places rapidly adopting Western lifestyles," explained study coauthor Julia Durack, PhD, Executive Director of the Holobiont Medical Research Foundation. "These diseases are much less common in traditional, non-industrialized communities. Because the skin microbiome is closely tied to skin health, we wanted to study the Yanomami, one of the last remaining hunter-gatherer groups, who rarely experience these conditions. By looking at their skin microbiome, we hoped to better understand what might be missing in modern populations and how that relates to the rise in skin disorders."
What they found was that the skin of this group who reside in the remote Amazonian rainforest share some bacterial communities with Western-nation populations, but with markedly greater species diversity (R2 =.455; P =.001).19 A total of 115 previously unknown bacterial genomes were identified as part of the skin microbiome of these individuals.
"The Yanomami community we worked with has had very limited contact with outsiders, so it's unlikely that the shared taxa we observed were introduced by westerners. Instead, these are what we would call conserved microbial groups — taxa that are commonly found across humans and even other mammals," Dr Durack said. "What was particularly interesting in our data was that while the Yanomami share some of these same microbial groups with Western populations, the diversity within those groups was much greater. For example, their skin harbored a wider range of Staphylococcus species, including ones we didn't detect at all on Western skin. That suggests their microbiomes are not only intact but also more complex, reflecting a deeper ecological richness rather than acquisition from outside contact."
That wasn't just a reflection of the Yanomami people living in the species-rich tropics, where there are more bacterial and fungal species in general, Dr Durack said.
"People living traditional lifestyles tend to have more species-diverse skin microbiomes, and this is consistent across non-industrialized groups worldwide, not only those in the tropics," she explained. "The key factor appears to be lifestyle rather than geography. In industrialized societies, our skin microbiomes are less diverse and compositionally distinct, shaped by constant exposure to chemicals, pollution, antibiotics, and a lack of contact with beneficial microbes from soil, plants, and other natural environments."
Dr Durack and other researchers refer to conditions like acne, rosacea, psoriasis, and atopic dermatitis as industrialized comorbidities, meaning they are strongly linked to the ecological and microbial shifts that come with modernization and not something inherent to genetics or ancestry, she said.
For example, other researchers found that when urban children in Finland have more natural play areas, their skin microbiome's species diversity grows within a few weeks, along with measurable changes in immune regulation markers.20
"This suggests that reintroducing environmental microbial exposures can directly influence health," Dr Durack said. "Our study extends this idea by showing that the Yanomami's continuous exposure to diverse environmental microbes likely helps maintain a complex skin microbiome. That complexity may be protective and its loss in industrialized societies could help explain the rise in inflammatory skin conditions we now consider hallmarks of modern living. Restoring microbial diversity on the skin could be an important way to boost resilience against inflammatory conditions."
The skin microbiome of a westernized adult who temporarily lived with the Yanomami shifted to Yanomami-like microbiomes, Dr Durack said, though it was lost upon their return to an industrialized setting.19
"That tells us it's not a closed door. Our skin microbiomes can adapt," she said. "In industrialized societies, we've largely lost this co-evolved relationship with our environment. While it may not be realistic to completely rewild our skin microbiomes to an ancestral state, Western medicine could take a more ecological approach: finding ways to reintroduce or support the right kinds of microbial exposures that strengthen the skin barrier and immune balance. This could open new avenues for preventive and therapeutic strategies in dermatology."
Challenges and Furthering the Research
Not surprisingly for an emerging field of knowledge, researchers caution that mechanistic uncertainties and gaps in methodological standardization must be addressed to strengthen preclinical research, and that large, well-designed, standardized clinical studies are needed to more clearly establish causality between the microbiomes and disease.21,22
Early work with targeted bacteriophage culling has been promising so far, but little is yet known about long-term effects on commensal species, the potential for evolved resistance to phages, or off-target effects on beneficial microbes.13
Nor do we yet know the best strategies for ecological engraftment (defined as sustained integration of introduced species into the skin microbiome) or how species diversity and composition might affect resistance to introduced species.7
Yet direct-to-consumer marketing hype has gotten well ahead of the science, Dr Gallo cautioned. "An unfortunate lack of scientific rigor has occurred that has led to false claims and unrealistic expectations," he said. "The field is working through this, but several products are still sold without good scientific evidence that they are effective."
The field has taken its first tentative steps, but has yet to find its stride. "We still need to define how specific microbes and their products shape skin and systemic immunity, and when dysbiosis becomes pathologic," Dr Archer said. "This includes microbe-neuro-immune interactions, which are only beginning to be uncovered in the skin with much to be discovered about how skin microbes may affect distal neural development."
We also don't yet understand what nutrients skin microbes use, or how exactly transitions between homeostatic and inflammatory states might cause metabolic shifts in the microbiome, he noted.
"Longitudinal, mechanistic, and multi-tissue studies will be essential to close these gaps," Dr Archer said. "We are currently investigating how pathogenic bacteria gain a foothold onto our skin and why certain pathogens are commonly prevalent among multiple inflammatory skin conditions.If we can understand the strategies by pathogens to live on our skin, we hope to prevent colonization and exacerbation of inflammatory skin disorders that involve dysbiosis."
"We're only just beginning to understand how important the skin microbiome is for our overall health," agreed Dr Durack. "Most of what we know so far is based on studies of people in industrialized societies, which gives us a very narrow view. By broadening research to include communities with diverse ethnicities, lifestyles, and environments, we can uncover much more relevant insights into what truly supports healthy skin — and how modern lifestyles may be limiting that potential."
Disclosure: Weiss Biosciences Inc. funded the Yanomami skin microbiome study and paid Dr Durack's salary. Dr Nathan Archer has received previous grant support from Pfizer and Boehringer Ingelheim and was a paid consultant for Janssen Pharmaceuticals and Alphyn Biologics. Dr Gallo had no relevant disclosures.
References:
- Chaudhary PP, Myles IA, Zeldin J, et al. Shotgun metagenomic sequencing on skin microbiome indicates dysbiosis exists prior to the onset of atopic dermatitis. Allergy. 2024;78(10):2724-2731. doi:10.1111/all.15806
- Kim HB, Alexander H, Um JY, et al. Skin microbiome dynamics in atopic dermatitis: understanding host-microbiome interactions. Allergy Asthma Immunol Res. 2025;17(2):165-180. doi:10.4168/aair.2025.17.2.165
- Asees A, Sadur A, Choudhary S. The skin microbiome in rosacea: mechanisms, gut-skin interactions, and therapeutic implications. Cutis. 2025;116(1):20-23. doi:10.12788/cutis/1240
- Niedzwiedzka A, Micallef MP, Biazzo M, Podrini C. The role of the skin microbiome in acne: challenges and therapeutic opportunities. Int J Mol Sci. 2024;25(21):11422. doi:10.3390/ijms.252111422
- Ruuskanen MO, Vats D, Potbhare R, et al. Towards standardized and reproducible research in skin microbiomes. Environ Microbiol. 2022;24(9):3840-3860. doi:10.1111/1462-2920.15945
- Li Chengchen, Ravikrishnan A, Wijaya I, et al. Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites. bioRxiv. Published online ahead of print June 8, 2025. doi:10.1101/2025.04.24.650393
- Oh J, Voigt AY. The human skin microbiome: from metagenomes to therapeutics. Nat Rev Microbiol. Published online August 4, 2025. doi:10.1038/s41579-025-01211-9
- Wilkhoo HS, Islam AW, Hussain S, Kadam SR, Rao ZK, Singh B. Skin microbiome and inflammatory dermatoses: a focused review. Costmoderma. 2025;5:107. doi:10.25259/CSDM_99_2025
- Huang C, Zhuo F, Han B, et al. The updates and implications of cutaneous microbiota in acne. Cell Biosci. 2023;13:113. doi:10.1186/s13578-023-01072-w
- Lyu Y, Shen J, Che Y, Dai L. Skin microbiome engineering: challenges and opportunities in skin disease treatment. iMetaOmics. 2025;2:e70012. doi:10.1002/imo2.70012
- Ito Y, Amagai M. Controlling skin microbiome as a new bacteriotherapy for inflammatory skin diseases. Inflamm Regen. 2022;42:26. doi:10.1186/s41232-022-00212-y
- Uberoi A, Murga-Garrido SM, Bhanap P, et al. Commensal-derived tryptophan metabolites fortify the skin barrier: insights from a 50-species gnotobiotic model of human skin microbiome. Cell Chem Biol. 2025;32(1):P111-P125.E6. doi:10.1016/j.chembiol.2024.12.007
- Natarelli N, Gahoonia N, Sivamani RK. Bacteriophages and the microbiome in dermatology: the role of the phageome and a potential therapeutic strategy. Int J Mol Sci. 2023;24(3):2695. doi:10.3390/ijms24032695
- Nakatsuji T, Chiang H, Jiang SB, Nagarajan H, Zengler K, Gallo RL. The microbiome extends to subepidermal compartments of normal skin. Nat Commun. 2013;4:1431. doi:10.1038/ncomms2441
- Nakatsuji T, Cheng JY, Gallo RL. Mechanisms for control of skin immune function by the microbiome. Curr Opin Immunol. 2021;72:324-330. doi:10.1016/j.coi.2021.09.001
- Dokoshi T, Chen Y, Cavagnero KJ, et al. Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice. Nat Commun. 2024;15:3009. doi:10.1038/s41467-024-47072-3
- Kline SN, Feller LE, Saito Y, et al. Epicutaneous Staphylococcus aureus initiates cross-tissue IL-36R signaling for neutrophilic lung inflammation in a model of the atopic march. Cell Reports. 2025;44(8):116054. doi:10.1016/j.celrep.2025.116054
- Wang G, Sweren E, Liu H, et al. Bacteria induce skin regeneration via IL-1β signaling. Cell Host Microbe. 2021;29(5):777-791.e6. doi:10.1016/j.chom.2021.03.003
- Durack J, Piceno Y, Vuong H, et al. Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin. Nat Comm. 2025;16:5542. doi:10.1038/s41467-025-60131-7
- Roslund MI, Puhakka R, Grönroos M, et al. Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children. Sci Adv. 2020;6(42):eaba2578. doi:10.1126/sciadv.aba2578.
- Metwaly A, Kriaa A, Hassani Z, et al. A consensus statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research. Nat Rev Gastroenterol Hepatol. 2025;22:343-356. doi:10.1038/s41575-025-01041-3
- Shahid U. Microbiome-guided precision medicine: mechanistic insights, multi-omics integration, and translational horizons. J Precis Med: Health Dis. 2025;3:100018. doi:10.1016/j.premed.2025.100018
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